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NM_000535.7(PMS2):c.1144+1del AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 27, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002456536.2

Allele description [Variation Report for NM_000535.7(PMS2):c.1144+1del]

NM_000535.7(PMS2):c.1144+1del

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.1144+1del
HGVS:
  • NC_000007.14:g.5989800del
  • NG_008466.1:g.24308del
  • NM_000535.7:c.1144+1delMANE SELECT
  • NM_001322003.2:c.739+1del
  • NM_001322004.2:c.739+1del
  • NM_001322005.2:c.739+1del
  • NM_001322006.2:c.988+2174del
  • NM_001322007.2:c.826+1del
  • NM_001322008.2:c.826+1del
  • NM_001322009.2:c.739+1del
  • NM_001322010.2:c.583+2174del
  • NM_001322011.2:c.211+1del
  • NM_001322012.2:c.211+1del
  • NM_001322013.2:c.571+1del
  • NM_001322014.2:c.1144+1del
  • NM_001322015.2:c.835+1del
  • NM_001406866.1:c.1330+1del
  • NM_001406868.1:c.1168+1del
  • NM_001406869.1:c.1036+1del
  • NM_001406870.1:c.988+2174del
  • NM_001406871.1:c.1144+1del
  • NM_001406872.1:c.1144+1del
  • NM_001406873.1:c.946+1del
  • NM_001406874.1:c.976+1del
  • NM_001406875.1:c.835+1del
  • NM_001406876.1:c.826+1del
  • NM_001406877.1:c.835+1del
  • NM_001406878.1:c.835+1del
  • NM_001406879.1:c.835+1del
  • NM_001406880.1:c.835+1del
  • NM_001406881.1:c.835+1del
  • NM_001406882.1:c.835+1del
  • NM_001406883.1:c.826+1del
  • NM_001406884.1:c.820+2174del
  • NM_001406885.1:c.808+1del
  • NM_001406886.1:c.778+1del
  • NM_001406887.1:c.739+1del
  • NM_001406888.1:c.739+1del
  • NM_001406889.1:c.739+1del
  • NM_001406890.1:c.739+1del
  • NM_001406891.1:c.739+1del
  • NM_001406892.1:c.739+1del
  • NM_001406893.1:c.739+1del
  • NM_001406894.1:c.739+1del
  • NM_001406895.1:c.739+1del
  • NM_001406896.1:c.739+1del
  • NM_001406897.1:c.739+1del
  • NM_001406898.1:c.739+1del
  • NM_001406899.1:c.739+1del
  • NM_001406900.1:c.679+2174del
  • NM_001406901.1:c.670+2174del
  • NM_001406902.1:c.670+2174del
  • NM_001406903.1:c.826+1del
  • NM_001406904.1:c.631+1del
  • NM_001406905.1:c.631+1del
  • NM_001406906.1:c.583+2174del
  • NM_001406907.1:c.583+2174del
  • NM_001406908.1:c.739+1del
  • NM_001406909.1:c.571+1del
  • NM_001406910.1:c.739+1del
  • NM_001406911.1:c.373+1del
  • NM_001406912.1:c.804-6808del
  • LRG_161t1:c.1144+1del
  • LRG_161:g.24308del
  • NC_000007.13:g.6029430del
  • NC_000007.13:g.6029431del
  • NM_000535.5:c.1144+1delG
Links:
dbSNP: rs2128746842
NCBI 1000 Genomes Browser:
rs2128746842
Molecular consequence:
  • NM_001322006.2:c.988+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406870.1:c.988+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406884.1:c.820+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406900.1:c.679+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406901.1:c.670+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406902.1:c.670+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406906.1:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406907.1:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406912.1:c.804-6808del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322003.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322004.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322005.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322007.2:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322008.2:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322009.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322011.2:c.211+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322012.2:c.211+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322013.2:c.571+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322014.2:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322015.2:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406866.1:c.1330+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406868.1:c.1168+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406869.1:c.1036+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406871.1:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406872.1:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406873.1:c.946+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406874.1:c.976+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406875.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406876.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406877.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406878.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406879.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406880.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406881.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406882.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406883.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406885.1:c.808+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406886.1:c.778+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406887.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406888.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406889.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406890.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406891.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406892.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406893.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406894.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406895.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406896.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406897.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406898.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406899.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406903.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406904.1:c.631+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406905.1:c.631+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406908.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406909.1:c.571+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406910.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406911.1:c.373+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002615799Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Feb 27, 2020) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002615799.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1144+1delG intronic variant is located one nucleotide after coding exon 10 and results from the deletion of one nucleotide (G) within intron 10 of the PMS2 gene. This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to shift the native splice donor site upstream by one nucleotide resulting in an out-frame deletion of one nucleotide at the end of coding exon 10; however, direct evidence is unavailable. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024